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Getting 'Exon' information from database.
1JI4
Asym. Unit
Info
Asym.Unit (307 KB)
Biol.Unit 1 (301 KB)
(using Jmol or JSmol)
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(1)
Title
:
NAP PROTEIN FROM HELICOBACTER PYLORI
Authors
:
G. Zanotti, E. Papinutto, W. G. Dundon, R. Battistutta, M. Seveso, G. Del Giudice, R. Rappuoli, C. Montecucco
Date
:
29 Jun 01 (Deposition) - 09 Oct 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.52
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Keywords
:
Dodecamer, Four-Helix Bundle, Metal Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Zanotti, E. Papinutto, W. G. Dundon, R. Battistutta, M. Seveso, G. Del Giudice, R. Rappuoli, C. Montecucco
Structure Of The Neutrophil-Activating Protein From Helicobacter Pylori
J. Mol. Biol. V. 323 125 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 36)
Info
All Hetero Components
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
1d: FE (III) ION (FEd)
1e: FE (III) ION (FEe)
1f: FE (III) ION (FEf)
1g: FE (III) ION (FEg)
1h: FE (III) ION (FEh)
1i: FE (III) ION (FEi)
1j: FE (III) ION (FEj)
1k: FE (III) ION (FEk)
1l: FE (III) ION (FEl)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
2d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
2e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
2f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
2g: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDg)
2h: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDh)
2i: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDi)
2j: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDj)
2k: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDk)
2l: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDl)
3a: UNKNOWN ATOM OR ION (UNXa)
3b: UNKNOWN ATOM OR ION (UNXb)
3c: UNKNOWN ATOM OR ION (UNXc)
3d: UNKNOWN ATOM OR ION (UNXd)
3e: UNKNOWN ATOM OR ION (UNXe)
3f: UNKNOWN ATOM OR ION (UNXf)
3g: UNKNOWN ATOM OR ION (UNXg)
3h: UNKNOWN ATOM OR ION (UNXh)
3i: UNKNOWN ATOM OR ION (UNXi)
3j: UNKNOWN ATOM OR ION (UNXj)
3k: UNKNOWN ATOM OR ION (UNXk)
3l: UNKNOWN ATOM OR ION (UNXl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
12
Ligand/Ion
FE (III) ION
2
MPD
12
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
UNX
12
Ligand/Ion
UNKNOWN ATOM OR ION
[
close Hetero Component info
]
Sites
(36, 36)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:25 , UNX A:802 , ASP D:52 , GLU D:56
BINDING SITE FOR RESIDUE FE D 801
02
AC2
SOFTWARE
HIS B:25 , UNX B:804 , ASP C:52 , GLU C:56
BINDING SITE FOR RESIDUE FE C 803
03
AC3
SOFTWARE
ASP B:52 , GLU B:56 , HIS C:25 , UNX C:806
BINDING SITE FOR RESIDUE FE B 805
04
AC4
SOFTWARE
ASP A:52 , GLU A:56 , HIS D:25 , UNX D:808
BINDING SITE FOR RESIDUE FE A 807
05
AC5
SOFTWARE
HIS E:25 , UNX E:810 , ASP H:52 , GLU H:56
BINDING SITE FOR RESIDUE FE H 809
06
AC6
SOFTWARE
HIS F:25 , UNX F:812 , ASP G:52 , GLU G:56
BINDING SITE FOR RESIDUE FE G 811
07
AC7
SOFTWARE
ASP F:52 , GLU F:56 , HIS G:25 , UNX G:814
BINDING SITE FOR RESIDUE FE F 813
08
AC8
SOFTWARE
ASP E:52 , GLU E:56 , HIS H:25 , UNX H:816
BINDING SITE FOR RESIDUE FE E 815
09
AC9
SOFTWARE
HIS I:25 , UNX I:818 , ASP L:52 , GLU L:56
BINDING SITE FOR RESIDUE FE L 817
10
BC1
SOFTWARE
HIS J:25 , UNX J:820 , ASP K:52 , GLU K:56
BINDING SITE FOR RESIDUE FE K 819
11
BC2
SOFTWARE
ASP J:52 , GLU J:56 , HIS K:25 , UNX K:822
BINDING SITE FOR RESIDUE FE J 821
12
BC3
SOFTWARE
ASP I:52 , GLU I:56 , HIS L:25 , UNX L:824
BINDING SITE FOR RESIDUE FE I 823
13
BC4
SOFTWARE
HIS A:37 , FE D:801 , LYS G:134
BINDING SITE FOR RESIDUE UNX A 802
14
BC5
SOFTWARE
HIS B:37 , FE C:803 , LYS E:134
BINDING SITE FOR RESIDUE UNX B 804
15
BC6
SOFTWARE
FE B:805 , HIS C:37 , LYS F:134
BINDING SITE FOR RESIDUE UNX C 806
16
BC7
SOFTWARE
FE A:807 , HIS D:37 , LYS H:134
BINDING SITE FOR RESIDUE UNX D 808
17
BC8
SOFTWARE
HIS E:37 , FE H:809 , LYS K:134
BINDING SITE FOR RESIDUE UNX E 810
18
BC9
SOFTWARE
HIS F:37 , FE G:811 , LYS I:134
BINDING SITE FOR RESIDUE UNX F 812
19
CC1
SOFTWARE
FE F:813 , HIS G:37 , LYS J:134
BINDING SITE FOR RESIDUE UNX G 814
20
CC2
SOFTWARE
FE E:815 , HIS H:37 , LYS L:134
BINDING SITE FOR RESIDUE UNX H 816
21
CC3
SOFTWARE
LYS C:134 , HIS I:37 , GLU L:56 , FE L:817
BINDING SITE FOR RESIDUE UNX I 818
22
CC4
SOFTWARE
HIS J:37 , FE K:819
BINDING SITE FOR RESIDUE UNX J 820
23
CC5
SOFTWARE
FE J:821 , HIS K:37
BINDING SITE FOR RESIDUE UNX K 822
24
CC6
SOFTWARE
LYS D:134 , GLU I:56 , FE I:823 , HIS L:37
BINDING SITE FOR RESIDUE UNX L 824
25
CC7
SOFTWARE
GLU A:46 , TYR A:99 , LEU A:132 , SER A:135
BINDING SITE FOR RESIDUE MPD A 700
26
CC8
SOFTWARE
GLU B:46 , TYR B:99 , LEU B:132 , SER B:135
BINDING SITE FOR RESIDUE MPD B 701
27
CC9
SOFTWARE
GLU C:46 , TYR C:99 , LEU C:132 , SER C:135
BINDING SITE FOR RESIDUE MPD C 702
28
DC1
SOFTWARE
GLU D:46 , TYR D:99 , LEU D:132 , SER D:135
BINDING SITE FOR RESIDUE MPD D 703
29
DC2
SOFTWARE
GLU E:46 , TYR E:99 , LEU E:132 , SER E:135
BINDING SITE FOR RESIDUE MPD E 704
30
DC3
SOFTWARE
GLU F:46 , TYR F:99 , LEU F:132 , SER F:135
BINDING SITE FOR RESIDUE MPD F 705
31
DC4
SOFTWARE
GLU G:46 , TYR G:99 , LEU G:132 , SER G:135
BINDING SITE FOR RESIDUE MPD G 706
32
DC5
SOFTWARE
GLU H:46 , TYR H:99 , LEU H:132 , SER H:135
BINDING SITE FOR RESIDUE MPD H 707
33
DC6
SOFTWARE
GLU I:46 , TYR I:99 , LEU I:132 , SER I:135
BINDING SITE FOR RESIDUE MPD I 708
34
DC7
SOFTWARE
GLU J:46 , TYR J:99 , LEU J:132 , SER J:135
BINDING SITE FOR RESIDUE MPD J 709
35
DC8
SOFTWARE
GLU K:46 , TYR K:99 , LEU K:132 , SER K:135
BINDING SITE FOR RESIDUE MPD K 710
36
DC9
SOFTWARE
GLU L:46 , TYR L:99 , LEU L:132 , SER L:135
BINDING SITE FOR RESIDUE MPD L 711
[
close Site info
]
SAPs(SNPs)/Variants
(14, 168)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_DPS_HELPY_001 (H9V, chain A/B/C/D/E/F/G/H/I/J/K/L, )
02: VAR_DPS_HELPY_002 (N35H, chain A/B/C/D/E/F/G/H/I/J/K/L, )
03: VAR_DPS_HELPY_003 (E46G, chain A/B/C/D/E/F/G/H/I/J/K/L, )
04: VAR_DPS_HELPY_004 (M50L, chain A/B/C/D/E/F/G/H/I/J/K/L, )
05: VAR_DPS_HELPY_005 (I58L, chain A/B/C/D/E/F/G/H/I/J/K/L, )
06: VAR_DPS_HELPY_006 (V59A, chain A/B/C/D/E/F/G/H/I/J/K/L, )
07: VAR_DPS_HELPY_007 (S70T, chain A/B/C/D/E/F/G/H/I/J/K/L, )
08: VAR_DPS_HELPY_008 (I73L, chain A/B/C/D/E/F/G/H/I/J/K/L, )
09: VAR_DPS_HELPY_009 (E80D, chain A/B/C/D/E/F/G/H/I/J/K/L, )
10: VAR_DPS_HELPY_010 (E97D, chain A/B/C/D/E/F/G/H/I/J/K/L, )
11: VAR_DPS_HELPY_011 (E97G, chain A/B/C/D/E/F/G/H/I/J/K/L, )
12: VAR_DPS_HELPY_012 (Y101H, chain A/B/C/D/E/F/G/H/I/J/K/L, )
13: VAR_DPS_HELPY_013 (K107E, chain A/B/C/D/E/F/G/H/I/J/K/L, )
14: VAR_DPS_HELPY_014 (Q140E, chain A/B/C/D/E/F/G/H/I/J/K/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_DPS_HELPY_001
*
H
9
V
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
H
9
V
02
UniProt
VAR_DPS_HELPY_002
*
N
35
H
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
N
35
H
03
UniProt
VAR_DPS_HELPY_003
*
E
46
G
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
E
46
G
04
UniProt
VAR_DPS_HELPY_004
*
M
50
L
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
M
50
L
05
UniProt
VAR_DPS_HELPY_005
*
I
58
L
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
I
58
L
06
UniProt
VAR_DPS_HELPY_006
*
V
59
A
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
V
59
A
07
UniProt
VAR_DPS_HELPY_007
*
S
70
T
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
S
70
T
08
UniProt
VAR_DPS_HELPY_008
*
I
73
L
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
I
73
L
09
UniProt
VAR_DPS_HELPY_009
*
E
80
D
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
E
80
D
10
UniProt
VAR_DPS_HELPY_010
*
E
97
D
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
E
97
D
11
UniProt
VAR_DPS_HELPY_011
*
E
97
G
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
E
97
G
12
UniProt
VAR_DPS_HELPY_012
*
Y
101
H
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
Y
101
H
13
UniProt
VAR_DPS_HELPY_013
*
K
107
E
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
K
107
E
14
UniProt
VAR_DPS_HELPY_014
*
Q
140
E
DPS_HELPY
---
---
A/B/C/D/E/F/G/H/I/J/K/L
Q
140
E
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 24)
Info
All PROSITE Patterns/Profiles
1: DPS_1 (A:25-41,B:25-41,C:25-41,D:25-41,E:...)
2: DPS_2 (A:51-65,B:51-65,C:51-65,D:51-65,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DPS_1
PS00818
Dps protein family signature 1.
DPS_HELPY
25-41
12
A:25-41
B:25-41
C:25-41
D:25-41
E:25-41
F:25-41
G:25-41
H:25-41
I:25-41
J:25-41
K:25-41
L:25-41
2
DPS_2
PS00819
Dps protein family signature 2.
DPS_HELPY
51-65
12
A:51-65
B:51-65
C:51-65
D:51-65
E:51-65
F:51-65
G:51-65
H:51-65
I:51-65
J:51-65
K:51-65
L:51-65
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1ji4a_ (A:)
1b: SCOP_d1ji4f_ (F:)
1c: SCOP_d1ji4g_ (G:)
1d: SCOP_d1ji4h_ (H:)
1e: SCOP_d1ji4i_ (I:)
1f: SCOP_d1ji4j_ (J:)
1g: SCOP_d1ji4k_ (K:)
1h: SCOP_d1ji4l_ (L:)
1i: SCOP_d1ji4b_ (B:)
1j: SCOP_d1ji4c_ (C:)
1k: SCOP_d1ji4d_ (D:)
1l: SCOP_d1ji4e_ (E:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ferritin
(232)
Protein domain
:
Dodecameric ferritin homolog
(44)
Helicobacter pylori, Nap [TaxId: 210]
(7)
1a
d1ji4a_
A:
1b
d1ji4f_
F:
1c
d1ji4g_
G:
1d
d1ji4h_
H:
1e
d1ji4i_
I:
1f
d1ji4j_
J:
1g
d1ji4k_
K:
1h
d1ji4l_
L:
1i
d1ji4b_
B:
1j
d1ji4c_
C:
1k
d1ji4d_
D:
1l
d1ji4e_
E:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1ji4A00 (A:1-144)
1b: CATH_1ji4B00 (B:1-144)
1c: CATH_1ji4K00 (K:1-144)
1d: CATH_1ji4L00 (L:1-144)
1e: CATH_1ji4C00 (C:1-144)
1f: CATH_1ji4D00 (D:1-144)
1g: CATH_1ji4E00 (E:1-144)
1h: CATH_1ji4F00 (F:1-144)
1i: CATH_1ji4G00 (G:1-144)
1j: CATH_1ji4H00 (H:1-144)
1k: CATH_1ji4I00 (I:1-144)
1l: CATH_1ji4J00 (J:1-144)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Helicobacter pylori. Organism_taxid: 210.
(1)
1a
1ji4A00
A:1-144
1b
1ji4B00
B:1-144
1c
1ji4K00
K:1-144
1d
1ji4L00
L:1-144
1e
1ji4C00
C:1-144
1f
1ji4D00
D:1-144
1g
1ji4E00
E:1-144
1h
1ji4F00
F:1-144
1i
1ji4G00
G:1-144
1j
1ji4H00
H:1-144
1k
1ji4I00
I:1-144
1l
1ji4J00
J:1-144
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Ferritin_1ji4L01 (L:4-144)
1b: PFAM_Ferritin_1ji4L02 (L:4-144)
1c: PFAM_Ferritin_1ji4L03 (L:4-144)
1d: PFAM_Ferritin_1ji4L04 (L:4-144)
1e: PFAM_Ferritin_1ji4L05 (L:4-144)
1f: PFAM_Ferritin_1ji4L06 (L:4-144)
1g: PFAM_Ferritin_1ji4L07 (L:4-144)
1h: PFAM_Ferritin_1ji4L08 (L:4-144)
1i: PFAM_Ferritin_1ji4L09 (L:4-144)
1j: PFAM_Ferritin_1ji4L10 (L:4-144)
1k: PFAM_Ferritin_1ji4L11 (L:4-144)
1l: PFAM_Ferritin_1ji4L12 (L:4-144)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Ferritin
(83)
Helicobacter pylori (Campylobacter pylori)
(1)
1a
Ferritin-1ji4L01
L:4-144
1b
Ferritin-1ji4L02
L:4-144
1c
Ferritin-1ji4L03
L:4-144
1d
Ferritin-1ji4L04
L:4-144
1e
Ferritin-1ji4L05
L:4-144
1f
Ferritin-1ji4L06
L:4-144
1g
Ferritin-1ji4L07
L:4-144
1h
Ferritin-1ji4L08
L:4-144
1i
Ferritin-1ji4L09
L:4-144
1j
Ferritin-1ji4L10
L:4-144
1k
Ferritin-1ji4L11
L:4-144
1l
Ferritin-1ji4L12
L:4-144
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
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RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
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Asym.Unit (307 KB)
Header - Asym.Unit
Biol.Unit 1 (301 KB)
Header - Biol.Unit 1
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